AMBER Archive (2003)

Subject: Re: AMBER: torsional restraints for groups of atoms

From: xiaolin cheng (cheng_at_ilion.bio.sunysb.edu)
Date: Wed Oct 22 2003 - 19:30:33 CDT

I have a modified amber8 version can handle angle or torsional restraints
defined by groups of atoms.

xiaolin

-----------------------------
Xiaolin Cheng
Department of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790

----- Original Message -----
From: "Anonymous" <omeroueh_at_nd.edu>
To: <amber_at_scripps.edu>
Sent: Sunday, October 19, 2003 1:42 PM
Subject: AMBER: torsional restraints for groups of atoms

> The question below was asked on the AMBER mailing list sometime ago, but I
could
> not find any reply to it. Is it currently possible to define torsional
> restraints defined by four groups of atoms within sander?
>
>
> >>I hope this goes through to the AMBER mailing list ... I have been
> >>having problems posting ...
> >>
> >>
> >>Question: Is it possible in sander to apply a torsional restraint on
> >>center of mass of 4 groups? The manual describes (see page 140, v 7.0)
> >>how a distance restraint can be applied between 2 COMs but does not say
> >>anything about a torsional restraint.
>
>
>
> Quoting "David A. Case" <case_at_scripps.edu>:
>
> > On Fri, Oct 17, 2003, Qing Zhang wrote:
> > >
> > > I hope the belly option can be improved because it
> > > will make computational cost much cheaper, especially
> > > for large systems with small interesting parts, such
> > > as ligand docking, protein tails. While restraints do
> > > not reduce computational cost.
> > >
> >
> > Note that the above statement is only true for pairwise potentials, and
> > hence is not directly applicable to either PME or GB, which are the two
> > main types of force field used in Amber.
> >
> > ..dac
> >
> > --
> >
> > ==================================================================
> > David A. Case | e-mail: case_at_scripps.edu
> > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > The Scripps Research Institute | phone: +1-858-784-9768
> > 10550 N. Torrey Pines Rd. | home page:
> > La Jolla CA 92037 USA | http://www.scripps.edu/case
> > ==================================================================
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>
>
>
>
>
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